Job ID = 5790871 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 789,342 reads read : 1,578,684 reads written : 789,342 reads 0-length : 789,342 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:08 789342 reads; of these: 789342 (100.00%) were unpaired; of these: 247 (0.03%) aligned 0 times 725449 (91.91%) aligned exactly 1 time 63646 (8.06%) aligned >1 times 99.97% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 67883 / 789095 = 0.0860 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 07:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 07:59:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:35: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 07:59:35: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 07:59:35: #1 total tags in treatment: 721212 INFO @ Wed, 22 Apr 2020 07:59:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:59:35: #1 tags after filtering in treatment: 721212 INFO @ Wed, 22 Apr 2020 07:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:35: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:35: #2 number of paired peaks: 289 WARNING @ Wed, 22 Apr 2020 07:59:35: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Wed, 22 Apr 2020 07:59:35: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:35: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:35: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:35: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:35: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 07:59:35: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 22 Apr 2020 07:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.05_model.r WARNING @ Wed, 22 Apr 2020 07:59:35: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:35: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 22 Apr 2020 07:59:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:59:35: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.05_summits.bed INFO @ Wed, 22 Apr 2020 07:59:38: Done! pass1 - making usageList (16 chroms): 11 millis pass2 - checking and writing primary data (596 records, 4 fields): 3 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 08:00:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:07: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:00:07: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:00:07: #1 total tags in treatment: 721212 INFO @ Wed, 22 Apr 2020 08:00:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:00:07: #1 tags after filtering in treatment: 721212 INFO @ Wed, 22 Apr 2020 08:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:00:07: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:07: #2 number of paired peaks: 289 WARNING @ Wed, 22 Apr 2020 08:00:07: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:07: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:07: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:07: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:07: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:07: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 08:00:07: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 22 Apr 2020 08:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.10_model.r WARNING @ Wed, 22 Apr 2020 08:00:07: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:07: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 22 Apr 2020 08:00:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:00:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:00:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.10_summits.bed INFO @ Wed, 22 Apr 2020 08:00:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 08:00:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:36: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:00:36: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:00:36: #1 total tags in treatment: 721212 INFO @ Wed, 22 Apr 2020 08:00:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:00:36: #1 tags after filtering in treatment: 721212 INFO @ Wed, 22 Apr 2020 08:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:00:36: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:36: #2 number of paired peaks: 289 WARNING @ Wed, 22 Apr 2020 08:00:36: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:36: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:36: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:36: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:36: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:36: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 08:00:36: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 22 Apr 2020 08:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.20_model.r WARNING @ Wed, 22 Apr 2020 08:00:36: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:36: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 22 Apr 2020 08:00:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:00:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:00:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550809/SRX5550809.20_summits.bed INFO @ Wed, 22 Apr 2020 08:00:39: Done! pass1 - making usageList (16 chroms): 9 millis pass2 - checking and writing primary data (214 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。